Whole genome analysis of Klebsiella pneumoniae T2-1-1 from human oral cavity.

Klebsiella pneumoniae T2-1-1 was isolated from the human tongue debris and subjected to whole genome sequencing on HiSeq platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession JAQL00000000.

Direct link to deposited data

http://www.ncbi.nlm.nih.gov/assembly/GCF_000710855.1/

Materials and methods

Klebsiella pneumoniae is one of the pathogenic bacteria responsible for major cause of nosocomial infection [1]. In this study, K. pneumoniae strain T2-1-1 was isolated from human oral cavity as described in Yin et al. [2]. This bacterium was purified using KG medium and maintained on Luria-Bertani medium at 37 °C. Total genomic DNA was extracted using Qiagen DNA mini kit (Qiagen) and eluted with elution buffer (Qiagen) [3]. The purity of the extracted DNA was checked with Nanodrop (Thermo Scientific) and quantified using Qubit (Invitrogen) fluorometer. Subsequently the DNA sequencing library was prepared using TruSeq DNA PCR free library preparation kit and sequenced on HiSeq 2000 (Illumina) [3]. The raw reads generated by the sequencer was paired, trimmed and de novo assembled with CLC Genomic Workbench (v6) [4]. The assembled genome was subjected to gene prediction using Prodigal and annotated on RAST server [5], [6].

Data description

Whole genome sequencing has generated 63,236,675 raw reads. The filtered reads was assembled into 166 contigs and the estimated genome size is 5,398,530 bp. The average coverage of the assembled genome is 1211 fold. The N50 of the genome is 59,500 bp and the G + C content of 57%. Prodigal has predicted 5114 coding sequence within the genome. These genes were annotated and classified into 573 subsystems (Fig. 1). Most of the annotated genes were involved in carbohydrate metabolism (831), amino acids and derivatives (535), cofactors, vitamins, prosthetic groups and pigments formations (323), RNA metabolism (228), cell wall and capsule development (210) (Fig. 1) which is necessary for the survival of a bacteria. The RAST results also show that this bacteria genome carries 138 potential virulence, disease and defense related genes (Fig. 1) which allows the bacteria to cause lethal diseases in human. However, in depth studies in the future is needed in order to confirm the virulence gene and invasion strategies of K. pneumoniae strain T2-1-1.

Fig. 1

Subsystems of Klebsiella pneumoniae strain T2-1-1 generated using RAST.

Nucleotide accession number

This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. JAQL00000000. The version described in this paper is the first version, JAQL01000000.

Conflict of interest

The authors clarified that this work and writing has no conflict of interest.

Specifications
Organism/cell line/tissue	Klebsiella pneumoniae
Strain	T2-1-1
Sequencer or array type	HiSeq (Illumina)
Data format	Analyzed
Experimental factors	Microbial strain
Experimental features	Whole genome analysis and gene annotation of Klebsiella pneumoniae T2-1-2
Consent	N/A
Sample source location	Debris on human tongue surface